In this doc, it is mentioned that
The following features aren't yet supported in the Developer Preview.
... ...
Publishing add-ins to the Office Store or Office 365 centralized deployment that use custom functions.
I just want to make sure it means that at the moment we cannot submit to Office Store any add-in that has custom functions; what we can do is only internally deploying add-ins with custom functions, right?
Your interpretation of that guidance in the documentation is correct. i.e., an add-in that uses custom functions cannot currently be published to the Office Store or via Office 365 centralized deployment.
For information about other ways to publish an add-in, see Deploy and publish your Office Add-in.